
@article{buenrostro_atacseq_2015,
	title = {{ATAC}‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide},
	volume = {109},
	issn = {1934-3639, 1934-3647},
	url = {https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471142727.mb2129s109},
	doi = {10.1002/0471142727.mb2129s109},
	shorttitle = {{ATAC}‐seq},
	abstract = {Abstract
            This unit describes Assay for Transposase‐Accessible Chromatin with high‐throughput sequencing ({ATAC}‐seq), a method for mapping chromatin accessibility genome‐wide. This method probes {DNA} accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription‐factor binding and nucleosome position. The method is a fast and sensitive alternative to {DNase}‐seq for assaying chromatin accessibility genome‐wide, or to {MNase}‐seq for assaying nucleosome positions in accessible regions of the genome. © 2015 by John Wiley \& Sons, Inc.},
	number = {1},
	journaltitle = {{CP} Molecular Biology},
	author = {Buenrostro, Jason D. and Wu, Beijing and Chang, Howard Y. and Greenleaf, William J.},
	urldate = {2023-12-23},
	date = {2015-01},
	langid = {english},
	file = {Buenrostro et al_2015_ATAC‐seq.pdf:D\:\\document\\storage\\TLRQ27SQ\\Buenrostro et al_2015_ATAC‐seq.pdf:application/pdf},
}

@article{cusanovich_single-cell_2018,
	title = {A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility},
	volume = {174},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867418308559},
	doi = {10.1016/j.cell.2018.06.052},
	pages = {1309--1324.e18},
	number = {5},
	journaltitle = {Cell},
	author = {Cusanovich, Darren A. and Hill, Andrew J. and Aghamirzaie, Delasa and Daza, Riza M. and Pliner, Hannah A. and Berletch, Joel B. and Filippova, Galina N. and Huang, Xingfan and Christiansen, Lena and {DeWitt}, William S. and Lee, Choli and Regalado, Samuel G. and Read, David F. and Steemers, Frank J. and Disteche, Christine M. and Trapnell, Cole and Shendure, Jay},
	urldate = {2023-12-23},
	date = {2018-08},
	langid = {english},
	file = {Cusanovich et al_2018_A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.pdf:D\:\\document\\storage\\DQ7HL39V\\Cusanovich et al_2018_A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.pdf:application/pdf},
}

@article{buenrostro_single-cell_2015,
	title = {Single-cell chromatin accessibility reveals principles of regulatory variation},
	volume = {523},
	issn = {0028-0836, 1476-4687},
	url = {https://www.nature.com/articles/nature14590},
	doi = {10.1038/nature14590},
	pages = {486--490},
	number = {7561},
	journaltitle = {Nature},
	author = {Buenrostro, Jason D. and Wu, Beijing and Litzenburger, Ulrike M. and Ruff, Dave and Gonzales, Michael L. and Snyder, Michael P. and Chang, Howard Y. and Greenleaf, William J.},
	urldate = {2023-12-23},
	date = {2015-07},
	langid = {english},
	file = {Buenrostro et al_2015_Single-cell chromatin accessibility reveals principles of regulatory variation.pdf:D\:\\document\\storage\\ME9LT8A9\\Buenrostro et al_2015_Single-cell chromatin accessibility reveals principles of regulatory variation.pdf:application/pdf},
}

@article{hu_single-cell_2023,
	title = {Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity},
	volume = {15},
	issn = {1868-7083},
	url = {https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-023-01574-x},
	doi = {10.1186/s13148-023-01574-x},
	abstract = {Abstract
            
              Background
              Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as the fundamental drivers of carcinogenesis. However, recent research has shed light on the crucial role of epigenomic alterations in various cell types present within the tumor microenvironment, suggesting their potential contribution to tumor formation and progression. Despite these significant findings, the progress in understanding the epigenetic mechanisms regulating tumor heterogeneity has been impeded over the past few years due to the lack of appropriate technical tools and methodologies.
            
            
              Results
              The emergence of single-cell sequencing has enhanced our understanding of the epigenetic mechanisms governing tumor heterogeneity by revealing the distinct epigenetic layers of individual cells (chromatin accessibility, {DNA}/{RNA} methylation, histone modifications, nucleosome localization) and the diverse omics (transcriptomics, genomics, multi-omics) at the single-cell level. These technologies provide us with new insights into the molecular basis of intratumoral heterogeneity and help uncover key molecular events and driving mechanisms in tumor development.
            
            
              Conclusion
              This paper provides a comprehensive review of the emerging analytical and experimental approaches of single-cell sequencing in various omics, focusing specifically on epigenomics. These approaches have the potential to capture and integrate multiple dimensions of individual cancer cells, thereby revealing tumor heterogeneity and epigenetic features. Additionally, this paper outlines the future trends of these technologies and their current technical limitations.},
	pages = {161},
	number = {1},
	journaltitle = {Clin Epigenet},
	author = {Hu, Yuhua and Shen, Feng and Yang, Xi and Han, Tingting and Long, Zhuowen and Wen, Jiale and Huang, Junxing and Shen, Jiangfeng and Guo, Qing},
	urldate = {2023-12-23},
	date = {2023-10-11},
	langid = {english},
	file = {Hu et al_2023_Single-cell sequencing technology applied to epigenetics for the study of tumor.pdf:D\:\\document\\storage\\62GEFHCR\\Hu et al_2023_Single-cell sequencing technology applied to epigenetics for the study of tumor.pdf:application/pdf},
}

@article{wilkinson_epigenetic_2023,
	title = {Epigenetic regulation of early human embryo development},
	volume = {30},
	issn = {19345909},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1934590923003314},
	doi = {10.1016/j.stem.2023.09.010},
	pages = {1569--1584},
	number = {12},
	journaltitle = {Cell Stem Cell},
	author = {Wilkinson, Amy L. and Zorzan, Irene and Rugg-Gunn, Peter J.},
	urldate = {2023-12-23},
	date = {2023-12},
	langid = {english},
	file = {Wilkinson et al_2023_Epigenetic regulation of early human embryo development.pdf:D\:\\document\\storage\\2N8YACLW\\Wilkinson et al_2023_Epigenetic regulation of early human embryo development.pdf:application/pdf},
}

@article{grandi_chromatin_2022,
	title = {Chromatin accessibility profiling by {ATAC}-seq},
	volume = {17},
	issn = {1754-2189, 1750-2799},
	url = {https://www.nature.com/articles/s41596-022-00692-9},
	doi = {10.1038/s41596-022-00692-9},
	pages = {1518--1552},
	number = {6},
	journaltitle = {Nat Protoc},
	author = {Grandi, Fiorella C. and Modi, Hailey and Kampman, Lucas and Corces, M. Ryan},
	urldate = {2023-12-23},
	date = {2022-06},
	langid = {english},
	file = {Grandi et al_2022_Chromatin accessibility profiling by ATAC-seq.pdf:D\:\\document\\storage\\PL4Q3W43\\Grandi et al_2022_Chromatin accessibility profiling by ATAC-seq.pdf:application/pdf},
}

@article{mansisidor_chromatin_2022,
	title = {Chromatin accessibility: methods, mechanisms, and biological insights},
	volume = {13},
	issn = {1949-1034, 1949-1042},
	url = {https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2143106},
	doi = {10.1080/19491034.2022.2143106},
	shorttitle = {Chromatin accessibility},
	pages = {238--278},
	number = {1},
	journaltitle = {Nucleus},
	author = {Mansisidor, Andrés R. and Risca, Viviana I.},
	urldate = {2023-12-23},
	date = {2022-12-31},
	langid = {english},
	file = {Mansisidor_Risca_2022_Chromatin accessibility.pdf:D\:\\document\\storage\\EDH6N8KQ\\Mansisidor_Risca_2022_Chromatin accessibility.pdf:application/pdf},
}

@article{zaret_micrococcal_2005,
	title = {Micrococcal Nuclease Analysis of Chromatin Structure},
	volume = {69},
	issn = {1934-3639, 1934-3647},
	url = {https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471142727.mb2101s69},
	doi = {10.1002/0471142727.mb2101s69},
	abstract = {Abstract
            This unit describes methodology for using micrococcal nuclease to investigate the presence of nucleosomes at a particular location in chromatin and to map the positions of nucleosomes at various levels of resolution. The approaches are readily adaptable to other probes of chromatin structure that cause {DNA} cleavage. Results obtained from such chromatin studies provide a structural view of the molecular environment of gene in their native context in cells.},
	number = {1},
	journaltitle = {{CP} Molecular Biology},
	author = {Zaret, Ken},
	urldate = {2023-12-24},
	date = {2005-01},
	langid = {english},
	file = {Zaret_2005_Micrococcal Nuclease Analysis of Chromatin Structure.pdf:D\:\\document\\storage\\DT8QM243\\Zaret_2005_Micrococcal Nuclease Analysis of Chromatin Structure.pdf:application/pdf},
}

@article{landt_chip-seq_2012,
	title = {{ChIP}-seq guidelines and practices of the {ENCODE} and {modENCODE} consortia},
	volume = {22},
	issn = {1088-9051},
	url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.136184.111},
	doi = {10.1101/gr.136184.111},
	abstract = {Chromatin immunoprecipitation ({ChIP}) followed by high-throughput {DNA} sequencing ({ChIP}-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global {ChIP} experiment. Through our experience in performing {ChIP}-seq experiments, the {ENCODE} and {modENCODE} consortia have developed a set of working standards and guidelines for {ChIP} experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how {ChIP} quality, assessed in these ways, affects different uses of {ChIP}-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the {ENCODE} (
              http://encodeproject.org/{ENCODE}/
              ) and {modENCODE} (
              http://www.modencode.org/
              ) portals.},
	pages = {1813--1831},
	number = {9},
	journaltitle = {Genome Res.},
	author = {Landt, Stephen G. and Marinov, Georgi K. and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E. and Bickel, Peter and Brown, James B. and Cayting, Philip and Chen, Yiwen and {DeSalvo}, Gilberto and Epstein, Charles and Fisher-Aylor, Katherine I. and Euskirchen, Ghia and Gerstein, Mark and Gertz, Jason and Hartemink, Alexander J. and Hoffman, Michael M. and Iyer, Vishwanath R. and Jung, Youngsook L. and Karmakar, Subhradip and Kellis, Manolis and Kharchenko, Peter V. and Li, Qunhua and Liu, Tao and Liu, X. Shirley and Ma, Lijia and Milosavljevic, Aleksandar and Myers, Richard M. and Park, Peter J. and Pazin, Michael J. and Perry, Marc D. and Raha, Debasish and Reddy, Timothy E. and Rozowsky, Joel and Shoresh, Noam and Sidow, Arend and Slattery, Matthew and Stamatoyannopoulos, John A. and Tolstorukov, Michael Y. and White, Kevin P. and Xi, Simon and Farnham, Peggy J. and Lieb, Jason D. and Wold, Barbara J. and Snyder, Michael},
	urldate = {2023-12-24},
	date = {2012-09},
	langid = {english},
	file = {Landt et al_2012_ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.pdf:D\:\\document\\storage\\WTDM5BM3\\Landt et al_2012_ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.pdf:application/pdf},
}

@article{song_dnase-seq_2010,
	title = {{DNase}-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells},
	volume = {2010},
	issn = {1940-3402, 1559-6095, 1559-6095},
	url = {http://www.cshprotocols.org/lookup/doi/10.1101/pdb.prot5384},
	doi = {10.1101/pdb.prot5384},
	shorttitle = {{DNase}-seq},
	abstract = {{INTRODUCTION}
            Identification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes such as cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping {DNase} I hypersensitive ({HS}) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. This method utilizes {DNase} I to selectively digest nucleosome-depleted {DNA} (presumably by transcription factors), whereas {DNA} regions tightly wrapped in nucleosome and higher-order structures are more resistant. The traditional low-throughput method for identifying {DNase} I {HS} sites uses Southern blots. Here, we describe the complete and improved protocol for {DNase}-seq, a high-throughput method that identifies {DNase} I {HS} sites across the whole genome by capturing {DNase}-digested fragments and sequencing them by high-throughput, next-generation sequencing. In a single experiment, {DNase}-seq can identify most active regulatory regions from potentially any cell type, from any species with a sequenced genome.},
	pages = {pdb.prot5384},
	number = {2},
	journaltitle = {Cold Spring Harb Protoc},
	author = {Song, Lingyun and Crawford, Gregory E.},
	urldate = {2023-12-24},
	date = {2010-02},
	langid = {english},
	file = {Song_Crawford_2010_DNase-seq.pdf:D\:\\document\\storage\\A7Y84IDC\\Song_Crawford_2010_DNase-seq.pdf:application/pdf},
}

@article{buenrostro_transposition_2013,
	title = {Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, {DNA}-binding proteins and nucleosome position},
	volume = {10},
	issn = {1548-7091, 1548-7105},
	url = {https://www.nature.com/articles/nmeth.2688},
	doi = {10.1038/nmeth.2688},
	pages = {1213--1218},
	number = {12},
	journaltitle = {Nat Methods},
	author = {Buenrostro, Jason D and Giresi, Paul G and Zaba, Lisa C and Chang, Howard Y and Greenleaf, William J},
	urldate = {2023-12-24},
	date = {2013-12},
	langid = {english},
	file = {Buenrostro et al_2013_Transposition of native chromatin for fast and sensitive epigenomic profiling.pdf:D\:\\document\\storage\\XQ8ZAGCJ\\Buenrostro et al_2013_Transposition of native chromatin for fast and sensitive epigenomic profiling.pdf:application/pdf},
}

@article{cusanovich_multiplex_2015,
	title = {Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing},
	volume = {348},
	issn = {0036-8075, 1095-9203},
	url = {https://www.science.org/doi/10.1126/science.aab1601},
	doi = {10.1126/science.aab1601},
	abstract = {Chromatin state and the single cell
            
              Identifying the chromatin state of any single cell, which may or may not have a different function or represent different stages relative to others collected within any single culture, experiment, or tissue, has been challenging. Cusanovitch
              et al.
              skirted previously identified technological limitations to identify regions of accessible chromatin at single-cell resolution. Combinatorial cellular indexing, a strategy for multiplex barcoding of thousands of single cells per experiment, was successfully used to investigate the genome-wide chromatin accessibility landscape in each of over 15,000 single cells.
            
            
              Science
              , this issue p.
              910
            
          , 
            Combinatorial indexing can identify chromatin states at single-cell resolution.
          , 
            Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated before biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from more than 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.},
	pages = {910--914},
	number = {6237},
	journaltitle = {Science},
	author = {Cusanovich, Darren A. and Daza, Riza and Adey, Andrew and Pliner, Hannah A. and Christiansen, Lena and Gunderson, Kevin L. and Steemers, Frank J. and Trapnell, Cole and Shendure, Jay},
	urldate = {2023-12-25},
	date = {2015-05-22},
	langid = {english},
	file = {Cusanovich et al_2015_Multiplex single-cell profiling of chromatin accessibility by combinatorial.pdf:D\:\\document\\storage\\X2GUHRJD\\Cusanovich et al_2015_Multiplex single-cell profiling of chromatin accessibility by combinatorial.pdf:application/pdf},
}

@article{lake_integrative_2018,
	title = {Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain},
	volume = {36},
	issn = {1087-0156, 1546-1696},
	url = {https://www.nature.com/articles/nbt.4038},
	doi = {10.1038/nbt.4038},
	pages = {70--80},
	number = {1},
	journaltitle = {Nat Biotechnol},
	author = {Lake, Blue B and Chen, Song and Sos, Brandon C and Fan, Jean and Kaeser, Gwendolyn E and Yung, Yun C and Duong, Thu E and Gao, Derek and Chun, Jerold and Kharchenko, Peter V and Zhang, Kun},
	urldate = {2023-12-25},
	date = {2018-01},
	langid = {english},
	file = {Lake et al_2018_Integrative single-cell analysis of transcriptional and epigenetic states in.pdf:D\:\\document\\storage\\KBTZPQ62\\Lake et al_2018_Integrative single-cell analysis of transcriptional and epigenetic states in.pdf:application/pdf},
}

@article{lu_atacgraph_2021,
	title = {{ATACgraph}: Profiling Genome-Wide Chromatin Accessibility From {ATAC}-seq},
	volume = {11},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2020.618478/full},
	doi = {10.3389/fgene.2020.618478},
	shorttitle = {{ATACgraph}},
	abstract = {Assay for transposase-accessible chromatin using sequencing data ({ATAC}-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current {ATAC}-seq tools follow chromatin immunoprecipitation sequencing ({ChIP}-seq) strategies that do not consider {ATAC}-seq-specific properties. To incorporate specific {ATAC}-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named {ATACgraph} for analyzing and visualizing {ATAC}-seq data. {ATACgraph} profiles accessible chromatin regions and provides {ATAC}-seq-specific information including definitions of nucleosome-free regions ({NFRs}) and nucleosome-occupied regions. {ATACgraph} also allows identification of differentially accessible regions between two {ATAC}-seq datasets. {ATACgraph} incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of {ATACgraph} modules. Overall, {ATACgraph} is an effective tool designed for {ATAC}-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. {ATACgraph} can be run on any {ATAC}-seq data with no limit to specific genomes. As validation, we demonstrated {ATACgraph} on human genome to showcase its functions for {ATAC}-seq interpretation. This software is publicly accessible and can be downloaded at
              https://github.com/{RitataLU}/{ATACgraph}
              .},
	pages = {618478},
	journaltitle = {Front. Genet.},
	author = {Lu, Rita Jui-Hsien and Liu, Yen-Ting and Huang, Chih Wei and Yen, Ming-Ren and Lin, Chung-Yen and Chen, Pao-Yang},
	urldate = {2023-12-25},
	date = {2021-01-13},
	file = {Lu et al_2021_ATACgraph.pdf:D\:\\document\\storage\\YY7HBWLW\\Lu et al_2021_ATACgraph.pdf:application/pdf},
}

@article{granja_archr_2021,
	title = {{ArchR} is a scalable software package for integrative single-cell chromatin accessibility analysis},
	volume = {53},
	issn = {1061-4036, 1546-1718},
	url = {https://www.nature.com/articles/s41588-021-00790-6},
	doi = {10.1038/s41588-021-00790-6},
	abstract = {Abstract
            
              The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R ({ArchR};
              https://www.archrproject.com/
              ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. {ArchR} provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, {DNA} element-to-gene linkage, transcription factor footprinting, {mRNA} expression level prediction from chromatin accessibility and multi-omic integration with single-cell {RNA} sequencing ({scRNA}-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, {ArchR} is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.},
	pages = {403--411},
	number = {3},
	journaltitle = {Nat Genet},
	author = {Granja, Jeffrey M. and Corces, M. Ryan and Pierce, Sarah E. and Bagdatli, S. Tansu and Choudhry, Hani and Chang, Howard Y. and Greenleaf, William J.},
	urldate = {2023-12-25},
	date = {2021-03},
	langid = {english},
	file = {Granja et al_2021_ArchR is a scalable software package for integrative single-cell chromatin.pdf:D\:\\document\\storage\\HXEZAJRS\\Granja et al_2021_ArchR is a scalable software package for integrative single-cell chromatin.pdf:application/pdf},
}

@article{lai_principles_2018,
	title = {Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing},
	volume = {562},
	issn = {0028-0836, 1476-4687},
	url = {https://www.nature.com/articles/s41586-018-0567-3},
	doi = {10.1038/s41586-018-0567-3},
	pages = {281--285},
	number = {7726},
	journaltitle = {Nature},
	author = {Lai, Binbin and Gao, Weiwu and Cui, Kairong and Xie, Wanli and Tang, Qingsong and Jin, Wenfei and Hu, Gangqing and Ni, Bing and Zhao, Keji},
	urldate = {2023-12-26},
	date = {2018-10},
	langid = {english},
	file = {Lai et al_2018_Principles of nucleosome organization revealed by single-cell micrococcal.pdf:D\:\\document\\storage\\DKZSHJ3V\\Lai et al_2018_Principles of nucleosome organization revealed by single-cell micrococcal.pdf:application/pdf},
}
